Hooah,
Certainly it is always risky to try and diagnose a relationship over the internet so certainly I may be way off base here, but...
When I read your post I can't help but projecting myself and people I know into your situation. What I would try to do here is decide what my goal is. You have a history with this person and it seems this history is possibly getting in the way of communicating. Is your history simply going to make any real communication difficult to the point where these discussions become mostly opportunities to inflict pain on each other?
Seems one critical piece of information would be, are you able to communicate well with her when the topics are not religious?
It is unclear are you together as a couple and living in the same house?
Were I in your place I think I would consider the tact of exploring religion together. The difficulty would be then if you could find avenues where religion was actually explored rather than dogmatically taught.